How do I read protein peaks within a gene?

Question

[dally]

I would like to read specific protein peaks (P53, Cdk9, etc) and annotate them in order to see if they are found on exons, introns, or exon-intron junctions within a gene. What I have done is download BED files of Exons and Introns in the a gene region and annotate them using Homer, however I want to find the same information for these individual proteins within these gene.

How would I go about doing that?